Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

SUMMARY: Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. AVAILABILITY AND IMPLEMENTATION: Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. CONTACT: piotr@cs.put.poznan.pl.

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets.

Systems biology approach to investigate biological phenomena seems to be very promising because it is capable to capture one of the fundamental properties of living organisms, i.e. their inherent complexity. It allows for analysis biological entities as complex systems of interacting objects. The first and necessary step of such an analysis is building a precise model of the studied biological system. This model is expressed in the language of some branch of mathematics, as for example, differential equations. During the last two decades the theory of Petri nets has appeared to be very well suited for building models of biological systems. The structure of these nets reflects the structure of interacting biological molecules and processes. Moreover, on one hand, Petri nets have intuitive graphical representation being very helpful in understanding the structure of the system and on the other hand, there is a lot of mathematical methods and software tools supporting an analysis of the properties of the nets. In this paper a Petri net based model of the hemojuvelin-hepcidin axis involved in the maintenance of the human body iron homeostasis is presented. The analysis based mainly on T-invariants of the model properties has been made and some biological conclusions have been drawn.

Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach.

Anemia of chronic disorders is a very important phenomenon and iron is a crucial factor of this complex process. To better understand this process and its influence on some other factors we have built a mathematical model of the human body iron homeostasis, which possibly most exactly would reflect the metabolism of iron in the case of anemia and inflammation. The model has been formulated in the language of Petri net theory, which allows for its simulation and precise analysis. The obtained results of the analysis of the model's behavior, concerning the influence of anemia and inflammation on the transferrin receptors, and hepcidin concentration changes are the valuable complements to the knowledge following from clinical research. This analysis is one of the first attempts to investigate properties and behavior of a not fully understood biological system on a basis of its Petri net based model.

Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer.

Prostate cancer is the second leading cause of cancer death in men in the developed world. A more sensitive and specific detection strategy for lethal prostate cancer beyond serum prostate specific antigen (PSA) population screening is urgently needed. Diagnosis by canine olfaction, using dogs trained to detect cancer by smell, has been shown to be both specific and sensitive. While dogs themselves are impractical as scalable diagnostic sensors, machine olfaction for cancer detection is testable. However, studies bridging the divide between clinical diagnostic techniques, artificial intelligence, and molecular analysis remains difficult due to the significant divide between these disciplines. We tested the clinical feasibility of a cross-disciplinary, integrative approach to early prostate cancer biosensing in urine using trained canine olfaction, volatile organic compound (VOC) analysis by gas chromatography-mass spectroscopy (GC-MS) artificial neural network (ANN)-assisted examination, and microbial profiling in a double-blinded pilot study. Two dogs were trained to detect Gleason 9 prostate cancer in urine collected from biopsy-confirmed patients. Biopsy-negative controls were used to assess canine specificity as prostate cancer biodetectors. Urine samples were simultaneously analyzed for their VOC content in headspace via GC-MS and urinary microbiota content via 16S rDNA Illumina sequencing. In addition, the dogs' diagnoses were used to train an ANN to detect significant peaks in the GC-MS data. The canine olfaction system was 71% sensitive and between 70-76% specific at detecting Gleason 9 prostate cancer. We have also confirmed VOC differences by GC-MS and microbiota differences by 16S rDNA sequencing between cancer positive and biopsy-negative controls. Furthermore, the trained ANN identified regions of interest in the GC-MS data, informed by the canine diagnoses. Methodology and feasibility are established to inform larger-scale studies using canine olfaction, urinary VOCs, and urinary microbiota profiling to develop machine olfaction diagnostic tools. Scalable multi-disciplinary tools may then be compared to PSA screening for earlier, non-invasive, more specific and sensitive detection of clinically aggressive prostate cancers in urine samples.

Structural analysis of a Petri net model of oxidative stress in atherosclerosis.

Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented. This model includes also some information about stoichiometric relationships between its components and covers all mentioned factors. For the model, a structural analysis based on invariants was made and biological conclusions are presented. Since the model contains inhibitor arcs, a heuristic method for analysis of such cases is presented. This method can be used to extend the concept of feasible t-invariants.

Material properties of ultra-high molecular weight polyethylene: Comparison of tension, compression, nanomechanics and microstructure across clinical formulations.

This is the first study to simultaneously measure material properties in tension, compression, nanoindentation as well as microstructure (crystallinity and lamellar level properties) across a wide variety of clinically relevant ultra-high molecular weight polyethylene (UHMWPE) formulations. Methodologies for the measurement of UHMWPE mechanical properties-namely elastic modulus, yield stress, yield strain, ultimate strength, energetic toughness, Poisson's ratio, hardness and constitutive variables-are evaluated. Engineering stress-strain behavior is compared to true stress-strain behavior for UHMWPE across a range of cross-linking and antioxidant chemistry. The tensile mechanical properties and constitutive behavior of UHMWPE are affected by resin type, antioxidant source and degree of cross-linking. Poisson's ratio is shown to be affected by resin type, antioxidant addition, and cross-linking dosage. Relationships between bulk mechanical properties from different measurement methodologies as well as microstructure are analyzed across all material formulations using Spearman rank correlation coefficients. Modulus and yield strength correlate in both tension and compression. Similarly, tensile and compressive properties including modulus and yield strength correlate strongly with crystallinity (Xc) and lamellar thickness (D). This work has broad application and provides a basis for interpreting the mechanical behavior of UHMWPE used in orthopedic implants.

Application of polymer-mesh device to remodel left ventricular-mitral valve apparatus in ischemic mitral regurgitation.

OBJECTIVES: Ischemic mitral regurgitation (IMR) results from ischemic left ventricular (LV) distortion and remodeling, which displaces the papillary muscles and tethers the mitral valve leaflets apically. The aim of this experimental study was to examine efficacy of an adjustable novel polymer filled mesh (poly-mesh) device to reverse LV remodeling and reduce IMR. METHODS: Acute (N = 8) and chronic (8 weeks; N = 5) sheep models of IMR were studied. IMR was produced by ligation of circumflex branches to create myocardial infarction. An adjustable poly-mesh device was attached to infarcted myocardium in acute and chronic IMR models and compared with untreated sham sheep. Two- and 3-dimensional echocardiography and hemodynamic measurements were performed at baseline, post IMR, and post poly-mesh (humanely killed). RESULTS: In acute models, moderate IMR developed in all sheep and decreased to trace/mild (vena contracta: 0.50 ± 0.09 cm to 0.26 ± 0.12 cm; P < .01) after poly-mesh. In chronic models, IMR decreased in all sheep after poly-mesh, and this reduction persisted over 8 weeks (vena contracta: 0.42 ± 0.09 cm to 0.08 ± 0.12 cm; P < .01) with significant increase in the slope of end-systolic pressure-volume relationship (1.1 ± 0.5 mm Hg/mL to 2.9 ± 0.7 mm Hg/mL; P < .05). There was a significant reduction in LV volumes from chronic IMR to euthanasia stage with poly-mesh compared with sham group (%end-diastolic volume change -20 ± 11 vs 15% ± 16%, P < .01; %end-systolic volume change -14% ± 19% vs 22% ± 22%, P < .05; poly-mesh vs sham group) consistent with reverse remodeling. CONCLUSIONS: An adjustable polymer filled mesh device reduces IMR and prevents continued LV remodeling during chronic follow-up.

Corneal Cross-Linking With Verteporfin and Nonthermal Laser Therapy.

PURPOSE: To test whether verteporfin with a nonthermal laser increases corneal mechanical stiffness and resistance to enzymatic degradation ex vivo. METHODS: Thirty human corneas (n = 5 per group) were treated with verteporfin alone (V), irradiated with nonthermal laser therapy (689 nm) alone (NTL), or received combined treatment of verteporfin with nonthermal laser therapy for 1 sequence (V+NTL1) or 6 sequences (V+NTL6) of 1 minute of NTL exposure. Positive controls were pretreated with 0.1% riboflavin/20% dextran every 3 to 5 minutes for 30 minutes and irradiated with ultraviolet light type A (λ = 370 nm, irradiance = 3 mW/cm) for 30 minutes using the Dresden protocol (R+UVA). Untreated corneas were used as negative controls. The corneal biomechanical properties were measured with enzymatic digestion, compression, creep, and tensile strength testing. RESULTS: V+NTL6- and R+UVA-treated corneas acquired higher rigidity and more pronounced curvature than untreated corneas. The stress-strain tests showed that V+NTL6 and R+UVA corneas became significantly stiffer than controls (P < 0.005). The V+NTL6 group seemed to be slightly stiffer than the R+UVA group, although the differences were not statistically significant. V+NTL6 corneas were found to have a significantly lower absolute creep rate (-1.87 vs. -3.46, P < 0.05) and significantly higher maximum stress values (7.67 vs. 3.02 P < 0.05) compared with untreated corneas. CONCLUSIONS: Verteporfin-NTL (V+NTL6) increases corneal mechanical stiffness and resistance to enzymatic collagenase degradation. Although a clinical study is needed, our results suggest that V+NTL6 induces corneal cross-linking and corneal biomechanical changes that are similar to those induced by standard corneal collagen cross-linking.

Notch fatigue of ultrahigh molecular weight polyethylene (UHMWPE) used in total joint replacements.

Ultrahigh molecular weight polyethylene (UHMWPE) has remained the primary polymer used in hip, knee and shoulder replacements for over 50 years. Recent case studies have demonstrated that catastrophic fatigue fracture of the polymer can severely limit device lifetime and are often associated with stress concentration (notches) integrated into the design. This study evaluates the influence of notch geometry on the fatigue of three formulations of UHMWPE that are in use today. A linear-elastic fracture mechanics approach is adopted to evaluate crack propagation as a function of notch root radius, heat treatment and Vitamin E additions. Specifically, a modified stress-intensity factor that accounts for notch geometry was utilized to model the crack driving force. The degree of notch plasticity for each material/notch combination was further evaluated using finite element methods. Experimental evaluation of crack speed as a function of stress intensity was conducted under cyclic tensile loading, taking crack length and notch plasticity into consideration. Results demonstrated that crack propagation in UHMWPE emanating from a notch was primarily affected by microstructural influences (cross-linking) rather than differences in notch geometry.

The long term behaviour of CFBC ash-water systems.

Circulating fluidized bed combustion (CFBC) ashes in contact with water, whether in liquid or vapour form, exhibit considerable chemical activity, which can continue for more than a year. From the point of view of the setting of CFBC ash-water mixtures and their behaviour, the formation of gypsum and of ettringite are important. The crystallisation of ettringite is associated with expansion of the set mass and absorption of water into the solids, but the ash-water system as a whole shrinks. The extent of ettringite formation is reduced if carbonation of free lime can take place. There is little carbonation if the set solids are covered by water but if contact with air is not restricted, the ettringite formed earlier slowly decomposes, its place being taken by calcite and gypsum. The fate of the aluminium from decomposed ettringite is uncertain; no new crystalline Al compounds are found. It appears that ultimately most analytical lime present can become carbonated. This is environmentally beneficial since it reduces chemical activity in the landfill, and reduces the amount of CO2 released due to limestone use. The main features of the behaviour of CFBC ash-water mixtures can be reproduced in model systems (CaO-Al2O3-CaSO4-H2O) but that of real ashes is complicated by the presence of silicates and possible interactions between silica and the strongly alkaline aqueous medium. Also, aluminates present in the ash are probably more active with respect to ettringite formation than pure aluminum hydroxide.

Development of a scale for estimating procedural distress in the newborn intensive care unit: the Procedural Load Index.

BACKGROUND: Infants in the newborn intensive care unit (NICU) are exposed to routine procedures that often cause distress and carry a negative burden or load on the infant's neurodevelopment. AIM: A ratio level index is introduced to estimate procedural load so as to begin to develop a system to monitor the intensity of distress associated with common NICU procedures. STUDY DESIGN: Two psychophysical methods, magnitude estimation (ME) and the general labeled magnitude scale (gLMS) were used to survey 86 clinicians via the internet to estimate the distress associated with 55 common NICU procedures. RESULTS: gLMS and ME estimations correlated highly across all procedures (r = 0.97). gLMS values were used to derive the procedural load index (PLI) as a ratio level estimation of procedural distress. CONCLUSION: The PLI ranks and differentiates distress among common NICU procedures more precisely than current tools. This methodology, if correlated with infant physiological indices and health outcomes, may be operationalized at the bedside to measure procedural distress, and help to guide the ideal timing to perform procedures and minimize their negative consequence.